mountainsort5

dendro_apps/spikeforestxyz/Dockerfile

@@ -15,6 +15,12 @@ RUN pip install lindi==0.3.4
 # Install sortingview
 RUN pip install sortingview==0.13.3
 
+# Install spikeinterface-pipelines from source, for now
+RUN git clone https://github.com/SpikeInterface/spikeinterface_pipelines.git && \
+    cd spikeinterface_pipelines && \
+    # git checkout dev && \
+    pip install -e .
+
 # Copy files into the container
 RUN mkdir /app
 COPY *.py /app/

dendro_apps/spikeforestxyz/main.py

@@ -3,6 +3,7 @@
 
 from dendro.sdk import App
 from recording_summary.recording_summary import RecordingSummaryProcessor
+from mountainsort5.mountainsort5 import Mountainsort5Processor
 
 app = App(
     name="spikeforestxyz",
@@ -13,6 +14,7 @@
 
 
 app.add_processor(RecordingSummaryProcessor)
+app.add_processor(Mountainsort5Processor)
 
 if __name__ == "__main__":
     app.run()

dendro_apps/spikeforestxyz/mountainsort5/mountainsort5.py

@@ -0,0 +1,26 @@
+from dendro.sdk import ProcessorBase, InputFile, OutputFile
+from dendro.sdk import BaseModel, Field
+
+
+class Mountainsort5Context(BaseModel):
+    input: InputFile = Field(description="Input .nwb.lindi.json file")
+    output: OutputFile = Field(description="Output .json file")
+
+
+class Mountainsort5Processor(ProcessorBase):
+    name = "spikeforestxyz.mountainsort5"
+    description = "Run mountainsort5 spike sorting on a recording."
+    label = "spikeforestxyz.mountainsort5"
+    tags = []
+    attributes = {"wip": True}
+
+    @staticmethod
+    def run(context: Mountainsort5Context):
+        from .run_mountainsort5 import run_mountainsort5
+
+        output_fname = 'output.nwb.lindi.json'
+        context.input.download(output_fname)
+        run_mountainsort5(
+            output_fname
+        )
+        context.output.upload(output_fname)